This invention relates the preparation of compounds useful as monomers in the preparation of polyamides, and more particularly to novel methods and novel intermediates for the preparation of 3-hydroxypyrrole monomers for polyamides that are useful in nucleotide sequence recognition.
Certain polyamides derived from heteroaryl amino acid monomers are capable of binding to dsDNA and have been found useful in the recognition of nucleotide sequences as well as other applications. See, for example, Dervan U.S. Pat. No. 5,998,140 and Urbach et al., xe2x80x9cSequence Selectivity of 3-Hyroxypyrrole/Pyrrole Ring Pairings in the DNA Minor Groove,xe2x80x9d J. Am. Chem. Soc., 1999, 121, 11621-11629. Polyamides containing various combinations of amino acid units respectively comprising pyrrole, hydroxypyrrole and imidazole moieties have been found particularly suitable for this purpose. G/C base pairs have been found to be complemented by the juxtaposed combination of N-methylimidazole/N-methylpyrrole, C/G pairs by N-methylpyrrole/N-methylimdazole, and T/A pairs by N-methylpyrrole/N-methylpyrrole or N-methyl-3-hydroxypyrrole/N-methylpyrrole. Polyamides containing these combinations can form intracellular complexes by complementation with sequences in dsDNA, the complementation being advantageously facilitated by providing a hairpin turn in the polyamide, or may be accomplished by using two amide oligomers.
Methods for the preparation of hairpin polyamide polymers and monomers useful in their synthesis are described in the above-cited Dervan patent and Urbach et al. article. An earlier article of Momose et al., xe2x80x9c3-Hydroxypyrrole. I. A General Synthetic Route to 4,5-Unsubstituted Alkyl 3-Hydroxypyrrole-2-carboxylates,xe2x80x9d Chem. Pharm. Bull., 26(7), 2224-2238 (1979) also describes methods for the preparation of amino acids derivatives of 3-hydroxypyrrole.
A particularly preferred monomer for the preparation of heteroaryl polyamides is the 3-hydroxypyrrole derivative corresponding to the formula 
wherein R1 is typically methyl, and Rb a protective group to block side reactions during the course of the polyamide synthesis. Urbach describes a method for producing such monomer in which ethyl 4-carboxyl-3-hydroxy-1-methylpyrrole-2-carboxylate is reacted with diphenylphosphoryl azide in the presence of triethylamine in acetonitrile to form the isocyanate which is thereafter reacted with benzyl alcohol to produce ethyl 4-[(benzyloxycarbonyl)amino]-3-hydroxy-1-methyl-2-carboxylate. The latter compound is reacted with methyl iodide in the presence of 4-dimethylaminopyridine and potassium carbonate in acetone to produce the 3-methoxy derivative, after which di(t-butyl) carbonate and 10% Pd/C are added to the mixture, and the mixture stirred under a hydrogen atmosphere to produce ethyl 4-[(t-butoxycarbonyl)amino]-3-methoxy-2-carboxylate. The latter compound is saponified to the 2-carboxylic acid, which is useful as a monomer in the synthesis of polyamides of the type effective in the sequence identification procedures described in Dervan U.S. Pat. No. 5,998,140 and the Urbach article.
In the synthesis of Urbach, the steps required to introduce a blocked 4-amino group have an adverse tendency to decarboxylate at the 4-position, especially in the presence of water. Thus, for satisfactory monomer synthesis per the Urbach route, it is necessary that measures be taken to substantially exclude moisture from the reaction mixture. Moreover, the synthesis described by Urbach involves release of nitrogen gas from the reaction mixture. Unless the reaction conditions are carefully controlled, the rate of gas release may potentially pose an operational hazard, particularly in large scale synthesis.
In synthesis of the polyamides, it is also important that the 3-hydroxy group be protected so that it does not participate in side reactions which produce branched or cross-linked polyamides that are less suitable for nucleotide recognition than are the unbranched polyamides described by Dervan and Urbach. After polymerization, the O-methyl group is removed since the free hyroxyl is the desired structure for use in nucleic acid binding. Although O-methylation provides very satisfactory protection of the 3-hydroxy group during the polymerization reaction, and is a preferred protective procedure for many applications, the O-methyl group can be difficult to remove after the polymerization is complete. It would, therefore, be useful to provide other protective groups which are effective to prevent branching or cross-linking during the polymerization but more susceptible to removal from the polyamide product.
Among the objects of the present invention may be noted the provision of a method for the preparation of heteroaryl amino acid monomers useful in the preparation of polyamides; the provision of such a method which avoids the loss of desired substituents from the heteraryl ring during the course of synthesis reactions; the provision of such a process which can be constantly operated without rapid gas release from any reaction step; the provision of alternative protective groups at the 3-position of a 3-hydroxypyrrole derivative; and the provision of novel intermediates useful in the synthesis of monomers for bioactive polyamides.
Briefly, therefore, the invention is directed to a process for the preparation of a compound of Formula II 
wherein R1 and R3 substituted or unsubstituted alkyl (preferably C1 to C6), alkenyl (preferably C2 to C6), alkynyl (preferably C2 to C6), aralkyl, or aryl; R2 is substituted or unsubstituted alkyl, alkenyl, alkynyl, aralkyl, aryl, alkylcarbonyl, haloalkylcarbonyl, aralkylcarbonyl, arylcarbonyl, alkoxycarbonyl, alkenoxycarbonyl, alkynoxycarbonyl, arylkoxycarbonyl, aryloxycarbonyl or substituted silyl; R4 is hydrogen or methyl; and R5 is a carbamate-forming blocking group. The process comprises reducing the nitro group of a compound of Formula IV 
wherein R1, R2, R3 and R4 are as defined above, thereby producing a compound of Formula III 
wherein R1, R2, R3 and R4 are as defined above. The compound of Formula III is contacted with a blocking group reagent thereby substituting a blocking group on the 4-amino group.
The invention is further directed to a process for the preparation of the compound of Formula III. The process comprises reducing the nitro compound of a group of Formula IV.
The invention is further directed to a process for the preparation of the compound of Formula IV. In this process a 3-hydroxypyrrole derivative corresponding to Formula V 
or the keto tautomer of the 3-hydroxypyrrole derivative, the keto tautomer corresponding to the structure 
wherein R1, R3 and R4 are as set forth above, with a blocking reagent effective to form an xe2x80x94OR2 group at the 3-position of the compound of Formula V.
The invention is further directed to a process for the preparation of a 3-hydroxypyrrole derivative corresponding to Formula V or the keto tautomer thereof (as corresponding to Formula Va). The process comprises contacting a compound of Formula VII with a reagent effective for promoting ring closure. The compound of Formula VII corresponds to the structure 
wherein R1, R3 and R4 are as defined above and xe2x80x94OR6 is a leaving group.
The invention is further directed to a process for the preparation of a compound corresponding to Formula VII. In this process a compound of Formula VIII is reacted with an N-substituted glycine ester corresponding to Formula IX. The compound of Formula VIII has the structure 
wherein R1 and R6 are as defined above and R7 is a leaving group. The compound of Formula IX has the structure
R1NHCH2C(O)OR3 
wherein R1 is as defined above.
The invention is further directed to a process for the preparation of the compound corresponding to Formula XI 
or the keto tautomer thereof 
wherein R1, R3, R4 and R5 are as defined above. The process comprises contacting a compound of Formula XII and/or the keto tautomer thereof with a blocking group reagent thereby substituting a blocking group on the 4-amino group. The compound of Formula XII has the structure 
The keto tautomer of Formula XII corresponds to Formula XIIa 
In both Formula XII and Formula XIIa, R1, R3 and R4 are as defined above.
The invention is further directed to a process for the preparation of a compound of Formula XII. The process comprises reducing a nitro group of a compound of Formula V or the keto tautomer of Formula V.
The invention is further directed to a compound corresponding to Formula XIV 
wherein R10 is selected from among hydrogen, substituted and unsubstituted alkyl (preferably C1 to C6), alkenyl (preferably C2 to C6), alkynyl (preferably C2 to C6), aralkyl, aryl, alkylcarbonyl, haloalkylcarbonyl, aralkylcarbonyl, arylcarbonyl, alkoxycarbonyl, alkenoxycarbonyl, alkynoxycarbonyl, aralkoxycarbonyl, aryloxycarbonyl and substituted silyl; and R1, R3 and R4 are as defined above.
The invention is further directed to a compound corresponding to Formula XV 
wherein R1, R3, R4 and R10 are as defined above; and the keto tautomer of Formula XV wherein R10 of Formula XV would otherwise be hydrogen.
The invention is further directed to a compound corresponding to Formula VII 
wherein R1, R3, R4 and R6 are as defined above.
The invention is further directed to a process for the preparation of a compound corresponding to Formula XVI 
wherein R15 is selected from among alkyl (preferably C1 to C6), alkenyl (preferably C2 to C6), alkynyl (preferably C2 to C6), aralkyl and aryl; and R1, R2, R3 and R4 are as defined above. The process comprises contacting a compound of Formula III with a carbonyl compound under conditions effective for the reaction of the 4-amino group of the compound of Formula III with the carbonyl compound, to produce the compound of Formula XVII 
and contacting the compound of Formula XVII with an alcohol of Formula XVIII
R15OH 
wherein R15 is selected from unsubstituted alkyl (preferably C1 to C6), alkenyl (preferably C2 to C6), alkynyl (preferably C2 to C6), aralkyl, and aryl; and R1, R2, R3 and R4 are as defined above.
The invention is further directed to a process for the preparation of a compound of Formula XIX 
wherein R1, R4 and R5 are as defined above; or the keto tautomer of such compound of Formula XIX. The process comprises hydrolyzing a compound of Formula XX by contacting it with a base. The compound of Formula XX has the structure 
wherein R1, R4 and R5 are as defined above.
The invention is further directed to the preparation of a compound of Formula XX. The process comprises reacting a compound of Formula XXI with a blocking reagent 
wherein R1 and R4 are as defined above.
The invention is further directed to the preparation of a compound of Formula XXI. The process comprises reducing the nitro group of a compound of Formula XXII 
wherein R1 and R4 are as defined above.
The invention is further directed to a process for the preparation of a compound corresponding to Formula XXII 
wherein R1 and R4 are as defined above. The process comprises reacting a compound of Formula V or the keto tautomer thereof with paraformaldehyde in the presence of a nitrogenous base.
The invention is further directed to a compound corresponding to the Formula XXII wherein R1 and R4 are as defined above.
The invention is further directed to a compound corresponding to Formula XXI 
wherein R1 and R4 are as defined above.
The invention is further directed to a compound corresponding to Formula XX 
wherein R1, R4 and R5 are as defined above.
The invention is further directed to a compound corresponding to Formula XXIII 
wherein R1, R4 and R5 are as defined above; and Rxe2x80x3 is selected from the group consisting of alkyl (preferably C1 to C6), alkenyl (preferably C2 to C6), alkynyl (preferably C2 to C6), aralkyl and aryl. R5 is preferably 
where R8 is selected from among substituted and unsubstituted alkyl (preferably C1 to C6), alkenyl (preferably C2 to C6), alkynyl (preferably C2 to C6), aralkyl and aryl.
The invention is further directed to a compound corresponding to the formula 
where R1, R4, R5 and R11 are as defined above.
The invention is further directed to a compound corresponding to Formula XXIV 
wherein R1, R4 and R5 are as defined above; and R12, R13 and R14 are independently alkyl (preferably C1 to C6).
Other objects and features will be in part apparent and in part pointed out hereinafter.
In accordance with the present invention, novel and advantageous processes are provided for the synthesis of heteroaryl amino acids. Novel intermediates are produced in the course of the various syntheses of the invention. The heteroaryl amino acid products of these syntheses are useful in the preparation of polyamides, e.g., hairpin polyamides, which bind to the minor groove of DNA and are effective for the identification of polynucleotide sequences.
As noted, the monomers ultimately used in the synthesis of dsDNA-complementing polyamides are 4-amino-3-hydroxy-2-carboxylic acids derivatives corresponding to the Formula XXV 
in which the 3-hydroxyl is protected by the Rb blocking group to prevent side reactions during polyamide synthesis. Although the monomers are typically unsubstituted in the 5-position, a substituent may optionally be present at this position provided that it creates no problems in polymerization arising from steric hindrance, electronic configuration, or reactivity. Preferably, the monomers are synthesized to also comprise a blocking substituent on the 4-amino group, i.e., the monomers correspond to the structure of Formula I 
wherein R1, R2, R4 and R5 are as defined above. In the course of solid phase polyamide synthesis, the R5 blocking group is removed at the N-terminus of the oligoamide immediately prior to coupling the next monomer unit, e.g., by treatment with trifluoroacetic acid.
In accordance with the invention, several alternative process schemes have been discovered for synthesis of 4-nitro-3-hydroxy-2-carboxylate esters and conversion thereof to 4-amino-3-hydroxy-2-carboxyate esters which are protected with blocking substituents at both the 3-position oxygen and and the 4-position nitrogen.
Each of the reaction schemes of the invention produces a monomer having the structure of Formula I 
In the structure of Formula I, R1 may independently be substituted and unsubstituted alkyl, alkenyl or alkynyl, preferably C1 to C6 alkyl, C2 to C6 alkenyl, or C2 to C6 alkynyl, and may also be aralkyl or aryl. For example, R1 may be methyl, ethyl, n-propyl, 1-propyl, n-butyl, 1-butyl, t-butyl, amyl and hexyl, vinyl, allyl, 2-butenyl, 3-pentenyl, ethynyl, phenyl, naphthyl and benzyl. Generally, alkyl groups are preferred, among which ethyl, 1-propyl and t-butyl are more preferred. Most preferably, R1 is methyl.
R2 in Formula I may be selected from among any of the substituents which may constitute R1, and may alternatively be substituted or unsubstituted alkylcarbonyl, aralkylcarbonyl, arylcarbonyl, haloalkylcarbonyl, alkoxycarbonyl, alkenoxycarbonyl, alkynoxcarbonyl, aralkoxycarbonyl, aryloxycarbonyl or substituted silyl. Preferably, R2 is methyl, allyl, or benzyl. Where R2 is further substituted, it may comprise any of the further substituents that are described above for substitution on R1.
R4 in Formula I is ordinarily hydrogen, but may alternatively be methyl.
R5 represents a carbamate-forming blocking group. Preferred blocking groups include t-butoxycarbonyl, fluorenylmethoxycarbonyl, allyloxycarbonyl, trialkylsilyloxycarbonyl, and benzyloxycarbonyl.
The several reaction schemes of the invention are described below.
Reaction Scheme 1
The first reaction scheme is advantageously initiated by the preparation of a precursor compound of Formula VIII 
wherein R4 is as defined above, R7 is a suitable leaving group, and xe2x80x94Oxe2x80x94R6 is a leaving group subject to removal in a subsequent ring closure reaction. R6 and R7 can be any of the constituents which may constitute R3 as described above. Preferably, R6 and R7 are independently C1 to C6 alkyl, more preferably methyl or ethyl, most preferably ethyl. In the preparation of the compound of Formula VIII, a nitroacetate ester compound corresponding to Formula X may be reacted with a trialkyl orthoformate or trialkyl orthoacetate, (e.g., triethyl orthoformate) and a carboxylic anhydride, preferably acetic anhydride. The substrate of Formula X has the structure
O2NCH2C(O)OR6xe2x80x83xe2x80x83(Formula X) 
where R6 is as defined above. Preferably, R6 is methyl or ethyl, more preferably ethyl. Generally, the preferred orthocarboxylate ester reactant comprises a lower alkyl ester, e.g., a trimethyl or triethyl ester. In the synthesis of heteroaryl amino acid monomers, an orthoformate triester is typically preferred. The reaction between the nitroacetate ester, orthoformate triester and acetic anhydride yields a compound of Formula VIII in which R4 is hydrogen. Use of the orthoacetate triester yields the corresponding compound in which R4 is methyl. The reaction is conducted under temperature and pressure conditions effective to drive off the by-product alcohol. Where a triethyl ester is used, the reaction may conveniently be conducted at atmospheric pressure and a temperature of between about 100xc2x0 and about 175xc2x0 C. Preferably, both orthoformate ester and acetic anhydride are introduced into the reaction zone in molar excess with respect to the nitroacetate ester substrate. After the reaction is complete, excess orthocarboxylate ester and carboxylic anhydride are removed, preferably under reduced pressure to yield the intermediate of Formula VIII.
In the next step of reaction scheme 1, the intermediate of Formula VIII is condensed with an N-substituted glycine reagent of Formula IX
R1NHCH2C(O)OR3xe2x80x83xe2x80x83(Formula IX) 
wherein R3 is as defined above, to yield a further intermediate of Formula VII 
wherein R1, R3, R4 and R6 are as defined above. Preferably, the N-substituted glycine reagent of Formula IX is a sarcosinate ester (i.e., R1 is methyl), more preferably ethyl sarcosinate (R3 is ethyl). Preferred moieties which can constitute R3 include those described above as groups which can constitute R1. The reaction is preferably conducted with substantially equimolar proportions of the compound of Formula VIII and the N-substituted glycine ester of Formula IX. The temperature of the reaction is not critical. Conveniently, it is conducted at room temperature under agitation and cooling for removal of the exothermic heat of reaction. Preferably, the reactants are co-fed to the reaction zone gradually over time, or one reactant is charged initially to the reaction zone and the other gradually added over time, so that the reaction rate and exotherm proceed at a controlled rate. If desired, the reaction can be conducted in a solvent medium such as water, dimethylsulfoxide, dimethylformamide, a lower alcohol such as ethanol or isopropanol, an aromatic solvent such as benzene, toluene, or xylene, or an ester such as ethyl acetate. However, maximum reactor payloads are provided where the reactants are introduced neat. Reaction time is typically under 2 hours. After the reaction is complete, by-product alcohol (R7OH) is removed by evaporation, yielding an oily liquid product.
Where the reaction of the compound of Formula VIII with the compound of Formula IX is conducted in a solvent, a product of enhanced purity may be obtained by extracting the product from the reaction medium, and then driving off the extraction solvent. For example, where the reaction is conducted in water, the product of Formula VII may be extracted in a more volatile solvent, e.g., ethyl acetate or an aromatic solvent. Where DMSO is the reaction medium, the product may be extracted with water. In the latter instance, the product may be recovered either by diluting water and back extracting into a more volatile solvent and recovering the product by driving off the latter solvent. The DMSO remains in the aqueous phase.
The compound of Formula VII is a novel compound useful in the synthesis of polyamides, and potentially useful as a multi-purpose intermediate and even as a monomer useful in preparation of polymers by addition polymerization. Where the compound of Formula VII is used in the synthesis of polyamides for binding to DNA, the substituents thereof are preferably selected on the basis outlined above. Most preferably R1 is methyl and R3 is ethyl. For such applications, the substituent R6, which is removed in a subsequent reaction step, is preferably C1 to C6 alkyl, most preferably methyl, propyl, isopropyl, n-butyl, or t-butyl, most preferably ethyl.
Ring closure of the intermediate of Formula VII yields the further novel intermediate of Formula V 
wherein R1, R3, and R4 are as set forth above. The compound of Formula V can exist in equilibrium with its keto tautomer 
For utility as an intermediate in preparation of monomers for polyamides that bind to DNA, there is no practical difference between the tautomers. In preparation of the compound of Formula V and/or Va, the compound of Formula VII is preferably contacted with a base effective for promoting the ring closure reaction. For example, the compound of Formula V/Va may be contacted with an alkali metal alkoxide in the presence of the alcohol, typically the alcohol corresponding to the alkoxide. The reaction may be conducted at ambient or elevated temperature, conveniently at atmospheric reflux in the alcohol medium. Heating may be required to sustain the desired reaction temperature. The alcohol medium is removed under reduced pressure to provide a residue comprising the crude alkali metal salt of the product of Formula V. The residue is taken up in water and acidified, e.g., with dilute sulfuric acid, to precipitate the 3-hydroxypyrrole derivative of Formula V and/or its keto tautomer of Formula Va.
Only the E isomer form of the compound of Formula VII undergoes ring closure to yield the salt of the compound of Formula V. Thus, unreacted Z isomer and reaction by-products are preferably removed from the precipitated compound of Formula V/Va. The precipitate is first separated from the acidified mother liquor by filtration or centrifugation, and washed with water, after which the washed solids are taken up in a solvent, preferably a halogenated solvent such as dichloromethane chloroform or 1,2-dichloroethane. The product may be passed through an adsorbent such as silica gel for further purification. The Formula V/Va product may be further purified, if desired, by recrystallization, e.g., from an ester/alkane solvent mixture.
In an alternative product recovery scheme, the 3-hydroxy compound of Formula V/Va can be precipitated directly by acidification of the reaction solution, after which the precipitate can be taken up in alkaline solution and the product extracted with an organic solvent such as an ether, ester, or halogenated solvent to remove neutral by-products. After acidification of the aqueous phase, the compound of formula IV/IVa can be extracted into an ether, ester or halogenated solvent. Removal of the solvent yields the product of Formula V/Va.
Optionally, bases other than an alkoxide can be used in the cyclization reaction. Certain of the other bases can be used if desired in a process in which a carbanion of Formula VIIa is first produced at low temperatures. 
wherein R1, R3, R4 and R5 are as defined above. For example, the carbanion may be initially produced by reaction in the cold in a solution comprising an organic solvent, the compound of Formula VII, and a base such as, e.g., Li or Na diisopropylamide or Li bis (trimethylsilylamide). Typically, a stable carbanion can be formed at temperatures in the range of xe2x88x9260xc2x0 C. to xe2x88x9290xc2x0 C. Warming the solution results in ring closure. This reaction may be conducted in any of a variety of solvents including tetrahydrofuran, benzene, toluene, and DMSO. The resulting solution containing a Li salt of the compound of Formula V may be treated with acid to precipitate the compound of Formula V and/or the tautomer of Formula Va. Formula V/Va product may be refined by taking up the precipitate in aqueous base, and extracting neutral by-products and Z isomer of Formula VII using an organic solvent such as ether, ethyl acetate or other low molecular weight ester, 1,2-dichloroethane or other halogenated solvent.
The compound of Formula V and its tautomer of Formula Va are novel compounds having utility in the synthesis of monomers for polyamides, and potentially for synthesis of other useful products. For use in synthesis of monomers for polyamides that bind to DNA, preferences for the substituents R1 and R3 of the compounds of Formula V/Va are the same as for corresponding substituents of the compounds of Formula VII.
In Reaction Scheme 1, the compound of Formula V and/or the tautomer of Formula Va are reacted with a reagent effective for introducing a blocking group R2 on the 3-hydroxyl, thereby producing a compound of Formula IV 
where R1, R2, and R3 are defined above. The reagent effective for introducing the blocking group is preferably an etherifying agent corresponding to the formula
(R2O)2SO4xe2x80x83xe2x80x83(Formula VI) 
or Formula VIa
R2Xxe2x80x83xe2x80x83(Formula VIa) 
where X is halo and R2 is defined above. The reaction is conducted under basic conditions, e.g., in the presence of an alkali metal carbonate or nitrogenous base. Where the etherifying agent is a halide (R2X), the substrate of Formula V may be converted to the 3-hydroxy salt, and thereafter reacted with R2X in the presence of an amine compound serving as a hydrogen halide scavenger. Where a sulfate etherifying agent is used, the reaction is preferably conducted in an organic solvent medium, e.g., a low molecular weight ketone in the presence of an alkali metal carbonate at a moderately elevated temperature, conveniently the atmospheric reflux temperature of the organic solvent. Acetone is particularly suitable. A substantial molar excess of (R2)2SO4 can be used to assure essentially quantitative conversion of the 3-hydroxy substrate of Formula V to the 3xe2x80x94OR2 intermediate product of Formula IV. However, it may be desirable to avoid a substantial excess in order to minimize consumption of the sulfate diester which can be difficult to recover economically, and may need to be destroyed after the etherification reaction is complete, e.g., by addition of aqueous ammonia. Thereafter, the product may be recovered by filtering to remove alkali metal carbonate and any other solid alkali metal salts, adding water to the filtered reaction mass and extracting the compound of Formula IV with an organic solvent of limited miscibility with water, e.g., diethyl ether. Preferably, the extract is washed with an alkaline solution before removal of the solvent by evaporation. The residue may be partially refined by taking it up in another solvent, preferably a halogenated solvent, and drying and filtering the resulting solution. The halogenated solvent is then removed by evaporation. Drying may be accomplished before or during evaporation of solvent by contacting the solution with a dessicant such as CaCl2 or by sparging with dry air or inert gas. The residue may be recrystallized as desired, preferably from a solvent comprising an alkane/ester mixture.
The compound of Formula IV is a novel compound having utility in the synthesis of monomers for polyamides, and potentially for synthesis of other useful products. For use in synthesis of monomers for polyamides that bind to DNA, preferences for the various substituents of the compound of Formula IV are the same as for compounds of Formula V.
The nitro group of the compound of Formula IV is then reduced to form a compound of Formula III 
wherein R1, R2 R3 and R4 are as defined above. Reduction of the nitro group may be accomplished by contacting the compound of Formula IV with a hydrogen transfer agent in the presence of a catalyst for the reduction reaction. A preferred catalyst is palladium, preferably on a carbon support. A typically suitable catalyst is 5% Pd/C or 10% Pd/C. A typical hydrogen transfer agents useful in the nitro reduction step is ammonium formate. The reaction is preferably conducted in an organic solvent, e.g., an ester such as ethyl acetate at moderately elevated temperature, conveniently at the atmospheric reflux temperature of the solvent. Alternatively, the reaction can be conducted in methanol at ambient temperature. A substantial excess of hydrogen transfer agent is preferably charged to the reaction to assure essentially quantitative reduction of the nitro group. An ester solvent such as ethyl acetate is especially preferred because it does not dissolve a hydrogen transfer agent such as ammonium formate, allowing excess transfer agent to be removed by filtration and recycled to the nitro reduction reactor. Reaction time is typically 20 to 60 minutes. The catalyst and excess undissolved hydrogen transfer agent are removed by filtration and the solvent evaporated, preferably under reduced pressure, for recovery of the product of Formula III.
Literature describing reduction of a nitro group on a heterocyclic ring with ammonium formate generally calls for a high weight ratio of catalyst to nitroheterocyclic substrate, e.g., a charge of 10% Pd/C catalyst essentially equal in weight to the substrate, or at least about 10% by weight Pd metal based on the substrate. In accordance with the invention, it has been discovered that reduction of the nitro group of compound IV can be accomplished using a relative low catalyst charge, i.e., a charge providing as low as 1% by weight Pd based on the substrate charge, or even lower. Preferably, the amount of catalyst charged to the reaction zone is between about 5% and about 1% by weight based on substrate, achieved for example by charging a 20% Pd/C catalyst in a proportion of between about 5% and about 25% by weight based on the substrate of Formula IV. The low catalyst charge provides advantages both in the consumption of catalyst and in facilitating the removal of catalyst by filtration.
Alternatively, reduction of the nitro group may be conducted by contacting the compound of Formula IV with hydrogen under pressure in the presence of a catalyst for the reaction. The same catalysts useful in the hydrogen transfer reaction can be used for catalytic hydrogenation. Substantially elevated hydrogen pressure is required for the reaction, e.g., 100 to 900 psig or higher. Conveniently, Formula IV substrate is charged to the reaction zone in an organic solvent solution. Reaction may be conducted at temperatures comparable to those used in the hydrogen transfer reaction.
The compounds of Formula III are novel compounds having utility in the synthesis of monomers for polyamides, and potentially for synthesis of other useful products. For use in synthesis of monomers for polyamides that bind to DNA, preferences for the various substituents of the compound of Formula III are the same as for compounds of Formula IV.
The compound of Formula III may be reacted with a blocking group reagent to produce a compound of Formula II 
wherein R5 represents a carbamate-forming blocking group and R1, R2, R3, and R4 are as defined above. Preferably, the blocking group reagent is a dicarbonate ester corresponding to the Formula 
where 
is R5 and R11 are independently selected from among substituted or unsubstituted alkyl (preferably C1 to C6), alkenyl (preferably C2 to C6), alkynyl (preferably C2 to C6), aralkyl or aryl, or substituted silyl. Preferred substituents which may constitute R8 include t-butyl, fluorenylmethyl, allyl, trialkylsilylmethyl and benzyl. Other substituents which may constitute R8 include those described above with respect to R2 and R3. Alternatively, the reaction may be conducted using an oxycarbonyl halide corresponding to the Formula
R8OC(O)X 
where 
and R8 are as defined above and X is halide.
In conducting the blocking reaction with a dicarbonate ester of Formula XIII, a solution of the compound of Formula III and dicarbonate ester is prepared, preferably in an aqueous solvent, more preferably in an acetone/water solvent mixture. Alternatively, another polar solvent, e.g., dioxane, can be used. Substantially quantitative blocking of the 4-amino group is promoted by charging at least a slight excess of the dicarbonate. The reaction proceeds satisfactorily at room temperature, preferably under neutral to basic conditions. The product may be recovered by extraction with a water-immiscible solvent, preferably a halogenated solvent such as dichloromethane, chloroform or 1,2-dichloroethane. The extract may be washed with water for removal of impurities, dried over a dessicant such as calcium chloride, or under vacuum or other convenient method, after which the solvent is removed by evaporation.
The compound of Formula II is converted to the compound of Formula I in a conventional manner, i.e., by saponification of the 2-carboxylate ester to the 2-carboxylic acid.
The overall synthesis of Reaction Scheme 1 thus proceeds according to the following series of reactions 
Reaction Scheme 2
Reaction scheme 2 proceeds in the same manner as reaction scheme 1 through the preparation of the intermediate compound of Formula V. The 4-nitro group of the compound of Formula V is then reduced to yield the compound of Formula XII 
As in the conversion of the compound of Formula IV to the compound of Formula III per reaction scheme 1, reduction of the Formula V compound nitro group can be accomplished by reaction with a hydrogen transfer agent such as ammonium formate in the presence of a catalyst for the reaction such as 5% or 10% Pd/C. Alternatively, the nitro reduction can be effected by catalytic hydrogenation under elevated hydrogen pressure. In either case the conditions for the reaction are essentially identical to those applicable to the preparation of the compound of Formula III from the compound of Formula IV.
The compounds of Formula XII are novel compounds having utility in the synthesis of monomers for polyamides, and potentially for synthesis of other useful products. For use in synthesis of monomers for polyamides that bind to DNA, preferences for the various substituents of the compounds of Formula XII are the same as for compounds of Formula V.
A blocking group is then introduced as a substituent on the 4-amino group of the compound of Formula XII, yielding a compound of Formula XI 
where R1, R3, R4 and R5 are as defined above. The reactions for preparation of the compound of Formula XI from the compound of Formula XII are the same as those described above per reaction scheme 1 for introducing a blocking group on the 4-amino substituent of the compound of Formula III to produce the compound of Formula II. Conditions for the reaction are also substantially the same as for the conversion of the Formula III compound to Formula II. In conversion of the compound of Formula XII to that of Formula XI, it is especially important to operate under neutral to acidic conditions to avoid reaction of the 3-hydroxyl group.
The compounds of Formula XI are novel compounds having utility in the synthesis of monomers for polyamides, and potentially for synthesis of other useful products. For use in synthesis of monomers for polyamides that bind to DNA, preferences for the substituents R1, R3, R4 and R5 of the compounds of Formula XI are the same as for compounds of Formula II.
The compound of Formula XI may be converted to the compound of Formula XIX by the same saponification reaction used for the conversion of the compound of Formula II to the compound of Formula I 
Preferably, the 4-amino blocking substituent and N-substituent (R1) of the compound of Formula XIX are the same as those of the compound of Formula I.
Although, the compound of Formula XIX may be used in the synthesis of polyamides, the 3-hydroxy group is preferably blocked also to prevent branching and crosslinking in the polymerization reaction. For this purpose, the compound of Formula XI is preferably reacted with a reagent which introduces such a protective group at the 3-position prior to saponification to the 2-carboxylic acid. The reagents and conditions for introduction of the protective group are the same as described above for the conversion of the compound of Formula V to the compound of Formula IV. When this reaction is conducted on the substrate of Formula XI, the O-protected product of the reaction is the compound of Formula II. Saponification of the compound of Formula II to the compound of Formula I is described above.
Thus, the overall synthesis of Reaction Scheme 2 is as follows 
When polyamides produced from the monomers of Formula I or XXV are used in DNA recognition, the O-protective group R2 must be removed. Although a methyl group functions effectively as the O-protective group R2 in the polymerization reaction, removal of a methyl group requires harsh conditions. Substituents such as acyl, trialkylsilyl, benzyl and allyl may be preferred in some cases.
Novel compounds of Formulae III and XII may be generically defined by Formula XIV 
and novel compounds of Formulae IV and V may be generically defined by Formula XV 
In each of Formulae XIV and XV R10 includes all groups that may constitute R2, plus hydrogen.
Reaction Scheme 3
In a further alternative reaction scheme of the invention, both the 3-hydroxy and 2-carboxy groups are blocked by formation of a fused ring compound of Formula XXII 
where R1 and R4 are defined above. The intermediate of Formula XXII is formed by reacting the compound of Formula V with paraformaldehyde in the presence of a base, preferably a nitrogenous base such as N,Nxe2x80x2-diisopropylethylamine (DIEA). The reaction may be carried out by heating the compound of Formula V with a several fold molar excess of paraformaldehyde in a polar solvent such as dimethylformamide or dimethyl sulfoxide at a temperature high enough to depolymerize the paraformaldehyde. Reaction temperature may typically range from about 25xc2x0 C. to about 150xc2x0 C.
The compound of Formula XXII is a novel intermediate useful in the synthesis of polyamides and potentially as an intermediate for other syntheses. Preferred substituents which may constitute R1 are the same as those for the other intermediates as described hereinabove.
The 4-nitro group of the compound of Formula XXII is reduced by catalytic reaction with a hydrogen transfer agent or by catalytic hydrogenation in the manner and under the conditions described hereinabove for the conversion of the compound of Formula IV to the compound of Formula III, thereby yielding the 4-amino compound of Formula XXI 
wherein R1 is as described above.
A blocking group is then introduced on the 4-amino group of the compound of Formula XXI to produce the compound of Formula XX 
wherein R1, R4 and R5 are as described above. Introduction of the blocking group is effected by the same reaction used to convert the compound of Formula III to the compound of Formula II. The reagents and conditions of the reaction are essentially the same as for the conversion of the compound of Formula III to Formula II, and the preferences in the nature of the blocking group are also the same.
The compounds of Formulae XX, XXI and XXII are novel compounds having utility in the synthesis of monomers for polyamides, and potentially for synthesis of other useful products. For use in synthesis of monomers for polyamides that bind to DNA, preferences for the substituents R1 and R5 of the compounds of Formulae XX, XXI and XXII are the same as for compounds of Formula II.
The compound of Formula XX may then be saponified to produce the compound of Formula XIX or a salt thereof. Saponification may be conducted by contacting the compound of Formula XX with 1-5 equivalents of an alkali metal hydroxide (e.g., LiOH, NaOH or KOH) in aqueous alcohol or aqueous DMSO. The reaction temperature may range from about 25xc2x0 C. to about 100xc2x0 C. and is preferably in the lower end of that range. LiOH is a preferred saponifying reagent.
The 3-hydroxy group may be protected by introducing an O-substituent with a trialkylsilyl chloride, aryl halide, or aryl anhydride and a suitable nitrogenous base in a nonpolar solvent. Suitable bases include pyridine, imidazole and trialkylamine. Suitable solvents include ethers, esters and haloalkanes.
Alternatively, the compound of Formula XIX may be reacted with a carboxylic acid anhydride of Formula XXVII 
where R8 and R11 are as defined above and may be the same or different, to produce a compound of Formula XXIII 
where R4, R5 and R11 are as defined above. An acyl halide such as R11C(O)Cl or R11C(O) Br can also be used. According to a still further option, a compound of Formula XIX may be reacted with a dicarbonate diester of Formula XIII 
or the haloformate:
R8OC(O)X 
where R8, R11 and X are as defined above to produce a compound of Formula XXVI: 
wherein R1, R4, and R5 are as defined above. Preferably R5 is R3xe2x80x94Oxe2x80x94C(O)xe2x80x94, where R8 is as defined above.
In accordance with a further alternative, the compound of Formula XIX may be reacted with a trialkylsilyl halide in the presence of a nitrogenous base to yield a compound of Formula XXIV: 
wherein R12, R13, and R14 are independently C1 to C6 alkyl and R1, R4 and R5 are as defined above. Again, R5 is preferably R8xe2x80x94Oxe2x80x94C(O)xe2x80x94.
The compounds of Formulae XXIII and XXIV are also novel compounds useful in the synthesis of monomers for polyamides, and potentially for synthesis of other useful products. For use in synthesis of monomers for polyamides that bind to DNA, preferences for the substituents R1 and R5 of the compound of Formulae XX, XXI and XXII are the same as for compounds of Formula II.
Thus, the overall synthesis of Reaction Scheme 3 is as follows: 
In providing the 4-amino group by reduction of a 4-nitro group, each of the above-described reaction schemes avoids the problem of 4-decarboxylation which is encountered when water is present in the synthesis of a blocked 4-amino group according the reaction scheme disclosed by Momose et al., supra.
Further in accordance with the present invention, another alternative reaction scheme is provided which can utilize a starting material comprising a 4-carboxyl pyrrole derivative.
Reaction Scheme 4
In reaction scheme 4 a compound corresponding to the Formula III: 
wherein:
R1, R2, R3 and R4 are as defined above;
is reacted with a carbonyl compound under conditions effective for the reaction of the 4-amino group of the compound of Formula III with the carbonyl compound, to produce a 4-isocyanate compound of Formula XVII: 
wherein R1, R2, R3, and R4 are as defined above. The carbonyl compound that reacts with the compound of Formula III is preferably a carbonyl compound comprising two leaving groups, more preferably a carbonyl dihalide such as phosgene, a phosgene dimer, i.e., trichloromethyl chloroformate, or a phosgene trimer, i.e., bis(trichloromethyl)carbonate. According to a still further alternative, the isocyanate may be formed by reacting the 4-amino group with CO2 in the presence of a dehydrating agent such as P2O5. The 4-isocyanate compound of Formula XVII may then reacted with an alcohol, e.g., t-butyl or benzyl alcohol to yield the compound of Formula XVI 
wherein R15 is unsubstituted alkyl (preferably C1 to C6), alkenyl (preferably C2 to C6), alkynyl (preferably C2 to C6), aralkyl or aryl, or substituted silyl; and R1, R2, R3 and R4 are as defined above. In carrying out this reaction, the isocyanate of Formula XVII is heated with a 1-5 fold molar excess of the alcohol in an aromatic solvent (e.g., toluene or xylene) in the presence of a nitrogenous base catalyst such as trialkylamine.
The compounds of Formula XVII are novel compounds having utility in the synthesis of monomers for polyamides, and potentially for synthesis of other useful products. For use in synthesis of monomers for polyamides that bind to DNA, preferences for the substituents R1, R2, R3, and R4 are the same as for compounds of Formula II, and the preferences are the same as the preferences for R2 in Formula II.
The overall synthesis of Reaction Scheme 4 is as follows: 
In a more preferred reaction scheme, the isocyanate of Formula XVII may be used directly in the preparation of polyamides. The isocyanate moiety of one monomer molecule reacts with the 2-carboxylate of another to form the amide linkage with extrusion of CO2.
The following examples illustrate the reactions.
Instrumentation and General Methods.
1H and 13C were recorded on a Varian VXR-300 (1H, 300 MHZ and 13C, 75.4 MHZ) or a Varian INOVA (1H, 400 MHZ and 13C, 100 MHZ) spectrometer in CDCl3 or DMSO-d6 as solvent unless otherwise stated. All NMR data are reported in ppm or d values downfield from tetramethylsilane (TMS, d=0.00, as an internal reference) and coupling constants, J, are reported in Hz. 13C NMR spectra were proton decoupled and recorded in CDCl3. The center peak of the solvent CDCl3 at 77.00 ppm was used as an internal reference. The multiplicities of the 13C NMR signals were determined by the attached proton test (APT) pulse sequence. Electron impact (EI) and chemical ionization (CI) mass spectra were recorded, at 70 eV ionizing voltage, on a Hewlett-Packard 5988A twin EI and CI quadrupole mass spectrometer connected to a Hewlett-Packard 5890A gas chromatograph fitted with a Hewlett-Packard 12 mxc3x970.33 mm Ultra-1 (cross-linked methyl silicone) column.
Low resolution liquid chromatography-mass spectrometry (LC-MS) experiments were performed utilizing a Hewlett Packard 1100 HPLC system and a Micromass Platform LCZ single quadrupole mass spectrometer with Electrospray as the ion source was operated in positive or negative mode. Exact mass measurements were performed on a Mariner T Biospectrometry(trademark) Workstation (Perceptive Biosystems, Inc.), time of flight (TOF) mass spectrometer. Molecular weight measurements have mass accuracies +/xe2x88x92100 ppm of the theoretical mass utilizing an external calibrant. The mass spectrometer was operated in positive mode using electrospray as the ion source.
Solutions were evaporated under reduced pressure with a rotary evaporator, and the residues were flash chromatographed on a silica gel column using an ethyl acetate/hexane mixture as the eluent unless specified otherwise. Chromatographic separations on the Chromatotron were accomplished using 2 mm or 4 mm Kieselgel 60 PF254 gypsum coated plates. Analytical thin-layer chromatography (TLC) analyses were performed on EM silica gel plates, 60PF254. Visualization was accomplished with UV light or iodine. Melting points were determined on a Dynamics Optics AHT 713921 hot-stage apparatus and are uncorrected. Microanalyses were performed by Atlantic Microlab, Inc., Norcross, Ga.
Materials and Reagents.
Sarcosine ethyl ester hydrochloride, triethylamine, ethyl nitroacetate, triethyl orthoformate, acetic anhydride, ethyl acetate, hexane, toluene, dimethyl sulfate, ammonium formate, Pd on activated charcoal (10%) and di-tert-butyldicarbonate, were obtained from Aldrich and used as such. Methylene chloride, dioxane, acetone, and tert-butyl alcohol were obtained from EM Science. Absolute ethyl alcohol (AAPER), sodium metal (Fisher), sodium hydroxide (J. T. Baker), ammonia (Matheson), diethyl ether and potassium carbonate (Mallinckrodt) were reagent grade and used as received.
Ethyl Sarcosinate (CH3NHCH2COOC2H5)
The liberation of the free ester from its hydrochloride salt was accomplished by passing dry ammonia gas through a suspension of sarcosine ethyl ester hydrochloride (50 g, 325.5 mmol) in diethyl ether (600 mL) at 0xc2x0 C. (ice-bath) for 3 h. Precipitated ammonium chloride was removed by filtration and washed with ether. The filtrate was concentrated, first by rotary evaporation and then on a vacuum pump for 30 min afforded ethyl sarcosinate as a pale pink liquid (38.55 g, 100%); 1H NMR (300 MHZ, CDCl3) d 1.28 (t, J=7.1 Hz, 3H, CH3xe2x80x94CH2xe2x80x94), 1.60 (s, 1H, CH3xe2x80x94NHxe2x80x94), 2.44 (s, 3H, CH3xe2x80x94NHxe2x80x94), 3.36 (s, 2H, xe2x80x94NHxe2x80x94CH2xe2x80x94), 4.20 (q, J=7.1 Hz, 2H, CH3xe2x80x94CH2xe2x80x94); 13C NMR (75.4 MHZ, CDCl3) d 14.19, 36.08, 52.65, 60.62, 172.32.